definecommon_air
Purpose:
This program will take a series of .air files that share a common standard
file and will define new .air files with a new standard file that represents
the "average" position, size and shape of the various reslice
files.
Usage:
definecommon_air input-prefix input-suffix
output-prefix output-suffix
overwrite?(y/n) id1
[..idN]
- where the following definitions apply:
- input-prefix
- a prefix that will be common to all of the input .air file names--use
"null" if you don't want a prefix
- input-suffix
- a suffix that will be common to all of the input .air file names--use
"null" if you don't want a suffix
- output-prefix
- a prefix that will be common to all of the output .air file names--use
"null" if you don't want an output prefix
- output-suffix
- a suffix that will be common to all of the output .air file names--use
"null" if you don't want an output suffix
- overwrite?(y/n)
- 'y' if you want preexisting output files with the same names as the
current output files to be overwritten
- id1
- unique identifier that appears in between the prefix and suffix
- ..idN
- additional unique identifiers
Examples:
definecommon_air null .airpet1 null .airpetcommon y pet1 pet2 pet3
pet4 pet5 pet6
- This command will average the six .air files pet1.airpet1 pet2.airpet1
pet3.airpet1 pet4.airpet1 pet5.airpet1 and pet6.airpet1. Six .air files
will be generated: pet1.aircommon, pet2.aircommon, pet3.aircommon, pet4.aircommon,
pet5.aircommon, and pet6.aircommon.
Comments:
- The output of this program is dependent upon the order in which the
input files are listed. This is due to the fact that certain aspects of
spatial averaging are not unique. As a result, there are multiple "correct"
solutions, one of which will be provided by this program.
- If you want to average a series of .air files that all have the same
reslice file instead of all having the same standard file, invert all of
the file using invert_air, apply this program to the results, and then invert
the output of this program.
Error messages: (alphabetical by case)
See also: Generic error messages
- WARNING: Potential standard file discrepancy .air file ____: ____
.air file ____: ____
- The .air files do not list the same standard file. If this is due
to the same file having two different names, you can ignore the warning.
- files ____ and ____ have incompatible standard file matrix dimensions
- The specified .air files do not agree about the matrix dimensions
of the standard file. They must agree to use this program.
- files ____ and ____ have incompatible standard file voxel sizes
- The specified .air files do not agree about the voxel sizes of the
standard file. They must agree to use this program.
- matrix ____ has an imaginary component
- You have possibly tried to average together files that represent spatial
inversions (mirror imaging) with files that do not. Review your input .air
files carefully. Note that the default identity matrix applied when you
specify a target-id other than "null" does not invert space. If
you are averaging files that do invert space, you must use the "null"
target-id.
- matrix ____ has dimensions ____ by ____ instead of 4x4
- WARNING: matrix in file _____ is not affine. Results are garbage
unless deviation from affine is trivial
- Review the specified .air file with scanair to verify that it uses
a nonaffine transformation. This program uses the fact that the transformations
are affine to compute matrix roots that are much stabler than would be possible
without this assumption.
See also:
Modified: December 22, 1995
© 1995 Roger P. Woods, M.D.(rwoods@ucla.edu)